Nmr-solve method for rapid identification of bi-ligand drug candidates

ABSTRACT

Methods for rapidly identifying drug candidates that can bind to an enzyme at both a common ligand site and a specificity ligand site, resulting in high affinity binding. The bi-ligand drug candidates are screened from a focused combinatorial library where the specific points of variation on a core structure are optimized. The optimal points of variation are identified by which atoms of a ligand bound to the common ligand site are identified to be proximal to the specificity ligand site. As a result, the atoms proximal to the specificity ligand site can then be used as a point for variation to generate a focused combinatorial library of high affinity drug candidates that can bind to both the common ligand site and the specificity ligand site. Different candidates in the library can then have high affinity for many related enzymes sharing a similar common ligand site.

This application is a continuation-in-part of application Ser. No.09/326,435, filed Jun. 4, 1999, the content of which is herebyincorporated by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to drug discovery methods, morespecifically to NMR methods for identifying atoms of interest in enzymeligands for generating and screening combinatorial libraries ofbi-ligand drug candidates.

2. Background Information

Widespread and sometimes indiscriminate use of antibiotics has allowedcertain strains of disease-causing bacteria to become resistant tocommonly available antibiotics. As a result, the need for more effectiveantimicrobial drugs is becoming more pressing. One approach todeveloping such drugs is to find compounds that bind to essentialenzymes in bacteria. When such enzymes have two adjacent binding sites,it is especially useful to find “bi-ligand” drugs that can bind at bothsites simultaneously. Such drugs are likely to bind extremely tightly,inactivating the enzyme and ultimately killing the bacteria.

The rapid discovery and development of bi-ligand drugs has beendifficult. Bi-ligand drug candidates have been identified using rationaldrug design, but previous methods are time-consuming and require aprecise knowledge of structural features. When searching for a drug thatbinds to an enzyme at two binding sites, it would be particularly usefulto understand how a ligand binds to the enzyme. Specifically, whichatoms in the ligand interact with which portions of the enzyme's bindingsites?

Recent advances in nuclear magnetic spectroscopy (NMR) have allowed thedetermination of the three-dimensional interactions between a ligand andan enzyme in a few instances. However, these efforts have been limitedby the size of the enzyme and can take years to map and analyze thecomplete structure of the complexes of enzyme and ligand.

Thus, there is a need to more rapidly identify which atoms in the ligandinteract with which portions of the enzyme binding sites so that focusedcombinatorial libraries can be generated and screened for more effectivedrugs. The present invention satisfies this need and provides relatedadvantages as well.

SUMMARY OF THE INVENTION

The present invention provides a method for rapidly identifying drugcandidates that can bind to an enzyme having at least two binding sites.The first site on the enzyme is the “common ligand site” where a knownligand can bind to the enzyme, as well as to other related enzymes. Thesecond site is a “specificity ligand site” adjacent to the common ligandsite. Thus, the method identifies bi-ligand drug candidates that canbind at both the common ligand site and the specificity ligand site. Asa result, the candidates can bind with high affinity to the enzyme. As afurther result, the candidates can be used to bind to related enzymessharing a similar common ligand site.

The bi-ligand drug candidates are screened from a combinatorial library.Like other combinatorial libraries, a number of diverse compounds can begenerated off of a core structure. In the case of a bi-ligand library,this core structure can be a mimic of the common ligand. The mimic canthen be derivatized with varying groups at a selected point to generatethe diversity of drug candidates in the library. The library is“focused” by optimizing the specific points on the mimic where variationoccurs.

The optimal points of variation on the ligand are identified bydetermining which atoms are proximal to the specificity ligand site whenthe mimic is bound to the common ligand site. These atoms are identifiedby first determining which amino acids of the enzyme are proximal to thespecificity ligand site, and then identifying which atoms on the boundcommon ligand mimic are proximal to these amino acids. NMR methods usingthe nuclear Overhauser effect (NOE) are particularly useful foridentifying proximal atoms. Accordingly, this technique has been namedNuclear Magnetic Resonance-Structure Oriented Library ValencyEngineering or NMR-SOLVE^(SM). As a result of NMR-SOLVE^(SM), theidentified proximal atoms can then be used as a point for variation togenerate a focused combinatorial library of high affinity drugcandidates that can bind to both the common ligand site and thespecificity ligand site of an enzyme of interest, as well as relatedenzymes sharing a similar common ligand site.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 a shows a schematic enzyme 1 having a specificity ligand site (SLsite) 1 a and a common ligand site (CL site) 1 b. For purposes ofillustration, an interface region 1 c is shown between the SL site 1 aand the CL site 1 b. Enzyme atom 1 d is within the interface region 1 cand enzyme atom 1 e is outside the interface region 1 c. FIG. 1 b showsa specificity ligand (SL) 2 bound to the SL site 1 a and a common ligand(CL) 3 bound to the CL site 1 b. The CL 3 has a reactive atom 3 a withina reactive region 3 b. A nonbound common ligand mimic (CL mimic) 4 isalso shown, having individual atoms 4 a, 4 b.

FIG. 2 illustrates the first stage of identifying an atom 1 d of theinterface region 1 c that is proximal to the reactive atom 3 a of the CL3. In FIG. 2 a, the reactive atom 3 a of the CL 3 is perturbed. In turn,a nearby atom 1 d in the interface region 1 c of the enzyme 1 becomesperturbed, as shown in FIG. 2 b. Atom 1 e, which is outside of theinterface region 1 c , is more distant from the reactive atom 3 a and isnot detectably perturbed. Thus, detection of the perturbation of nearbyatom 1 d allows its identification as an atom proximal to the reactiveatom 3 a of the CL 3.

FIG. 3 illustrates the second stage of identifying which CL mimics areproximal to the interface region 1 c and identifying an atom 4 a of theCL mimic 4 that is proximal to the part of the interface region 1 cidentified as 1 d. In FIG. 3 a, the atom 1 d previously identified inthe interface region 1 c is perturbed. An atom 4 a in the CL mimic 4then becomes perturbed, as shown in FIG. 3 b, but not atom 4 b, which ismore distant from interface atom 1 d. Consequently, an atom 4 a of theCL mimic 4 is identified that is proximal to the part of the interfaceregion 1 c identified as 1 d. As a further benefit, FIG. 3 c illustratesthat the second stage can determine whether a particular CL mimic 5binds to the CL site 1 b, but does not bind proximally to the interfaceregion 1 c. Thus, if interface atom 1 d is perturbed, it will be toodistant from atoms of the distally binding CL mimic 5 so that atom 5 adoes not become perturbed

Once a proximal atom 4 a has been identified in the CL mimic 4, FIG. 4 aillustrates a focused combinatorial library 6 of bi-ligand drugcandidates 6 a, 6 b, 6 c and 6 d, having varying substituent groupsattached to the identified proximal atom 4 a. These are in contrast todrug candidates 7 a to 7 h from an unfocused combinatorial library 7based on substitutions at other atoms such as 4 b of the CL mimic 4 orsubstitutions to a distally binding CL mimic 5. Upon screening thefocused library 6, a particular drug candidate 6 c is selected for highbinding affinity to the enzyme. As shown in FIG. 4 b, the drug candidate6 c consists of the CL mimic 4 attached to a SL-binding moiety 8 througha linker 9. The drug candidate 6 c can then bind the enzyme 1 tightly atboth the SL site 1 a and the CL site 1 b

FIG. 5 illustrates a variant method for identifying a proximal atom 4 a.In FIG. 5 a, a CL 3 is bound to the CL site 1 b in the presence ofnonbound CL mimic 4. An atom 3 a of the CL 3 is perturbed withradiofrequency irradiation, transferring energy to a nearby atom 1 d ofthe interface region 1 c in an NOE experiment. The CL 3 then unbinds, asin FIG. 5 b. In FIG. 5 c, a CL mimic 4 then binds to the CL site 1 b, sothat the energy is then transferred from the atom 1 d of the interfaceregion 1 c to a nearby atom 4 a of the CL mimic 4, as shown in FIG. 5 d.As a result, the variant method allows identification of an atom 4 a ofthe CL mimic 4 that is proximal to the interface region 1 c.

FIG. 6 illustrates the identification of amino acids at the interfaceregion. FIG. 6 a shows the results of a 2D-HSQC NMR experiment withTROSY for an NADH-bound dehydrogenase. FIG. 6 b shows the results of acomparable experiment with an NADD-bound dehydrogenase, where the NADDhas a deuterium-for-hydrogen substitution on the 4-carbon position ofthe nicotinamide ring. As is well known, the 4-carbon of NADH is closeto the interface region of dehydrogenases. In both figures, the x-axisrepresents the ¹H chemical shift and the y-axis represents the ¹⁵Nchemical shift. As a result of chemically perturbing the NADH to NADD,changes in the chemical shifts—represented by the two arrows—permitidentification of amino acids at the interface region of the enzyme.

FIG. 7 illustrates the identification of the proximal atom in the CLmimic using 3D-HSQC NOESY with TROSY. In FIG. 7 a, the horizontal axisrepresents the ¹H chemical shift of protein, the vertical axisrepresents the ¹⁵N chemical shift of protein and the oblique axisrepresents all ¹H chemical shifts. The broken arrows in FIG. 7 arepresent NOEs 10 resulting from radio frequency irradiation of thesample. These NOEs 10 are to ligand proton with chemical shift 11 TheNOEs 10 allow identification of a proximal atom 4 a of a CL mimic, shownin FIG. 7 b.

FIGS. 8 to 13 illustrate the results discussed in Example II.

FIG. 8 a shows the 2-D structure of the CL mimic designatedTTE0001.002.D2. The positions of protons H1, H2, H3, H4, G1, G2 and G3on the CL mimic are indicated. FIG. 8 b shows a Lineweaver-Burk plot forthe compound in competition with NADH for lactate dehydrogenase.

FIG. 9 shows the 2-D structures of the SL mimic2,6-pyridinedicarboxylate (2,6-PDC) (FIG. 9 a), the common ligand NADH(FIG. 9 b), and CL analog ACNADH (FIG. 9 c), which is used forperturbation by chemical modification ACNADH differs from NADH by asubstitution from amine in NADH to methyl in ACNADH, shown at the farright of FIGS. 9 b and 9 c. Furthermore, individual protons H_(1′A),H_(8A) and H_(2N) on ACNADH and corresponding atoms on NADH areindicated.

FIG. 10 illustrates step (a) of the method of the invention, showing¹H-¹³C HMQC spectra of threonine-labeled apo DHPR in the absence ofligand (FIG. 10 a), in the presence of common ligand NADH (FIG. 10 b)and in the presence of CL analog ACNADH. Peaks 2 and 12 are indicatedwith arrows.

FIG. 11 provides a chemical shift list of threonine residues in DHPR.The list separately provides the ¹H and ¹³C chemical shifts for freeDHPR (from FIG. 10 a), DHPR bound to common ligand NADH (from FIG. 10 b)and DHPR bound to CL analog ACNADH (from FIG. 10 c). Cross-peaks werearbitrarily assigned numbers. The list then tabulates the changes in ¹³Cand ¹H shifts between free DHPR and DHPR bound to NADH (Δδav NADH), andthen tabulates the changes between free DHPR and DHPR bound to AcNADH(Δδav AcNADH). The shifts were quantitated according to the starredequations shown. Shifts were normalized for proton (÷1.44) and carbon(÷33.7) chemical shift dispersion in the methyl region. The differencesbetween these comparisons are further compared (Δδav NADH versus ΔδavAcNADH) to identify potential atoms in the interface region.

FIG. 12 also illustrates step (a) of the invention, showing the 2D-NOESYspectrum of the binary complex of DHPR with CL analog AcNADH. The mixingtime was 200 msec. Atoms of AcNADH are as defined in FIG. 9 c. Chemicalshift A corresponds to a methyl group on a threonine in a part of the CLsite remote from the interface region that is close to atoms H_(8A) andH_(1′A) in AcNADH. In contrast, chemical shift B is for the atomcorresponding to cross-peak #2 in FIG. 10 c, with a proton chemicalshift of 1.5 ppm. This atom is close to proton H_(2N) in AcNADH, therebyconfirming H_(2N) as an proton proximal to the interface region.

FIG. 13 illustrates step (b) of the method of the invention. The 2DNOESY spectrum is of the ternary complex of DHPR with the CL mimicTTE0001.002.D2 (FIG. 8 a) and an SL analog, 2,6-PDC (see FIG. 9 a). TheSL analog was used to promote a closed conformation for the enzyme. Theatoms of TTE0001.002.D2 are as defined in FIG. 8 a. Cross-peak #2corresponds to cross-peak #2 in FIG. 10 c. There is a slightly differentproton chemical shift because SL mimic 2,6-PDC is bound, as well asbecause the CL mimic rather than AcNADH is bound. As a result, H1 isidentified as an atom on the CL mimic TTE0001.002.D2 proximal theinterface region, since H1 is known to have a proton chemical shift of7.0 ppm from independent assignments using 2D COSY and 1D protonspectra.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods for generating focusedcombinatorial libraries and for screening them for drug candidates thatcan bind tightly to certain enzymes. The libraries are “focused” byselecting the best core structures and optimizing the location ofvariations applied to a given core structure, which serves as a platformfor the particular library. Focusing the variations to a limited set ofpoints on the core structure reduces the number of compounds to begenerated and accelerates the drug discovery process. Using a corestructure that binds to a common site shared by members of a gene familycan also make the library generally useful for the other members. Thevariations in each library can be optimized by identifying specificatoms of interest in the core structure. For the purposes of theinvention, the core structure is a ligand—or a chemical mimic to such aligand—that binds to an enzyme.

The term “enzyme” herein means any protein that catalyzes a biochemicalreaction. Proteins having non-amino-acid modifications such asglycosylation or containing other non-proteinaceous components such asmetal ion prosthetic groups are included within this definition.

Enzymes useful in the invention are not limited by their size. Forexample, an enzyme can have a monomer molecular weight greater than 15,25, 30, 35 or 45 kD. An enzyme can also have a complete molecular weightgreater than 30, 50, 75, 100 or 150 kD. An enzyme can also have amonomer molecular weight less than 120, 100, 80, 60 or 40 kD, or acomplete molecular weight less than 200, 150, 100 or 50 kD. The term“molecular weight” herein means the sum of the atomic weights of all theatoms in the molecule. The molecular weight can be estimated using wellknown techniques such as SDS-PAGE under reducing or non-reducingconditions. Molecular weights can also be determined using massspectrometry, such as FAB, which includes cesium ion bombardment,electrospray ionization (ESI) and matrix-assisted laser desorptionionization (MALDI).

The enzyme can be obtained from any natural source such as humansubjects, primates, mammals, animals, plants, fungi or bacteria,including any derived cell or tissue cultures. In particular, the enzymecan be from a human or animal pathogen. An enzyme can also be derivedoriginally from a natural source, but later modified by artificialmeans, for example a recombinant enzyme or chemically modified enzyme.

The enzyme can also be a member of a gene family. The term “gene family”herein means a group of genes—or proteins encoded by such genes—oftenderived by duplication and variation from a common ancestral gene,exhibiting sequence homology and related phenotypic functions. Morespecifically, a gene family is a family of proteins that can all bind acommon ligand such as NADH or ATP. As such, gene family members canoften be identified by the presence of a conserved amino acid sequencemotif. Several large gene families have been identified, includingfamilies as large as 20, 50, 100 and even 200 members. Two particularexamples of a gene family are kinases and oxidoreductases. The term“kinase” herein means any enzyme that catalyzes the transfer of aphosphoryl group from ATP or other nucleoside triphosphate to anothercompound. The term “oxidoreductase” herein means any enzyme thatcatalyzes an oxidation-reduction reaction. Still other gene familiesinclude transaminases, decarboxylases and methyltransferases, as well asfamilies of farnesyl-, geranyl-, geranyl-geranyl- andubiquitin-transferring enzymes.

Another particular gene family is the dehydrogenase gene family. Theterm “dehydrogenase” herein means any enzyme that catalyzes the removalof hydrogen from a substrate using a compound other than molecularoxygen as an acceptor. Typically the hydrogen is transferred to thecoenzyme NAD⁺ (nicotinamide adenine dinucleotide) or NADP⁺ (nicotinamideadenine dinucleotide phosphate). The dehydrogenase gene family is large,comprising approximately 17% of all enzymes (You, Kwan-sa,“Stereospecificity for Nicotinamide Nucleotides in Enzymatic andChemical Hydride Transfer Reactions,” CRC Crit. Rev. Biochem. 17:313-451(1985)). A particularly useful enzyme is dihydrodipicolinate reductase(DHPR), which is 28 kD in monomer form, and is a tetramer in solution.Thus, the dehydrogenase family is likely to be a rich source of drugtargets.

The three-dimensional structures of several dehydrogenases are known,including dogfish lactate dehydrogenase, soluble porcine malatedehydrogenase, horse liver alcohol dehydrogenase, lobsterglyceraldehyde-3-phosphate dehydrogenase and Bacillus stearothermophilusglyceraldehyde-3-phosphate dehydrogenase (apo form). Based on thesestructures, it is now understood that dehydrogenases share severalconserved features, including two characteristic domains.

The first domain conserved among the dehydrogenases contains a site thatcan bind NAD⁺, NADP⁺ or a similar hydrogen acceptor (Bellamacina, C. R.,“The Nicotinamide Dinucleotide Binding Motif: A Comparison of NucleotideBinding Proteins,” FASEB J. 10:1257-1269 (1996)). Because the NAD⁺ligand that can bind at such a site is shared in common with othermembers of the gene family, the NAD⁺-binding site can be described as acommon ligand site. The term “common ligand site” herein means alocation on any enzyme where a common ligand can bind.

The term “common ligand” or “CL” herein means a molecule that canselectively bind at a site on an enzyme. A particularly useful CL canbind to a site conserved in a family of enzymes. The term can thereforeextend to molecules that can bind to members of a gene family.

A useful CL is a cofactor. The term “cofactor” herein means any smallmolecule that can bind in the CL site and participates in catalysis whenbound to an enzyme. Cofactors often contain a nucleotide such as adeninemononucleotide or nicotinamide mononucleotide. Examples of suchcofactors include ATP, ADP and SAM (S-adenosyl methionine). Anothergroup of cofactors that contain a nucleotide is the group NAD⁺, NADH,NADP⁺ and NADPH. Other such cofactors include FMNH₂, FMN, FAD, FADH₂,CoA, GTP and GDP. Still other cofactors include THF, DHF, TPP, biotin,dihydropterin, heme, farnesyl and farnesyl-pyrophosphate, geranyl,geranyl-geranyl, ubiquitin, pyridoxal phosphate and thiaminepyrophosphate.

CLs can have at least one atom that participates in the reactionmechanism catalyzed by the enzyme. In the case of NADH, this “reactiveatom” is a hydrogen atom attached to the carbon-4 position of thenicotinamide ring, which is transferred as a hydride ion For purposes ofdefinition, a “reactive region” of the common ligand can be defined toencompass the reactive atom as well common ligand atoms that areimmediately adjacent to the reactive atom. The reactive region alsoencompasses atoms of the common ligand that are immediately adjacent tothe specificity ligand. In this definition, “immediately adjacent” meanswithin 5 Ångstroms, but can be within 2, 3, 4 or 6, 7 or 8 Ångstroms. Infunctional terms, it can also mean sufficiently close that a chemicalperturbation in one atom can be detected in a second atom, using NMRmethods disclosed in greater detail below. Thus, a reactive region canmean the reactive atom itself as well as atoms of the common ligand thatare immediately adjacent to the reactive atom or common ligand atomsimmediately adjacent the SL. Since the reactive atom of a CL can reactwith an SL chemically, it is located at the interface of the CL and SLbinding sites at some point in time.

Although the common ligands can be naturally occurring cofactors ormolecules, the term also extends to chemical analogs that serve asmimics of the common ligand. Thus, “common ligand” should be understoodto encompass “common ligand mimics.”

The term “ligand mimic” herein means a molecule that can bind to theenzyme at the same site as the ligand. Thus, a CL mimic can displace aCL bound to an enzyme at the CL site. This property can be demonstratedby enzyme-binding competition assays between a natural common ligand anda common ligand mimic. The term can encompass molecules having portionssimilar to corresponding portions of the ligand in terms of structure orfunction. Because CLs can include CL mimics that are analogs ofnaturally occurring CLs, and because the scope of the term “CL mimic”can also encompass the original CL itself, the scope of the terms “CL”and “CL mimic” should be considered coextensive.

Examples of mimics to the common ligand NADH, for example cibacron blue,are described in Dye-Ligand Chromatography, Amicon Corp., LexingtonMass. (1980). In the case of cibacron blue, the similarity with NADH maynot be immediately obvious from schematic drawings of their chemicalstructures, and may only become apparent when their three-dimensionalstructures are compared. Thus, even when it is known that cibacron bluecan bind at NADH-binding sites on an enzyme, it may be difficult toassign correspondences between particular atoms in the CL and the CLmimic.

Numerous other examples of NADH-mimics, including useful modificationsto obtain such mimics, are described in Everse et al. (eds.), ThePyridine Nucleotide Coenzymes, Academic Press, New York N.Y. (1982).Particular analogs include nicotinamide 2-aminopurine dinucleotide,nicotinamide 8-azidoadenine dinucleotide, nicotinamide 1-deazapurinedinucleotide, 3-aminopyridine adenine dinucleotide,3-diazoacetylpyridine adenine dinucleotide and 5-aminonicotinamideadenine dinucleotide. Particular CL mimics can be identified andselected by ligand-displacement assays, as is well known in the art. CLmimic candidates can also be identified by searching databases ofcompounds for structural similarity with the common ligand or a CLmimic.

An example of a naturally occurring CL is NADH (FIG. 9 b). Another CL isAcNADH (FIG. 9 c), which is an analog of NADH. An example of a CL mimicis shown in FIG. 8 a. When a CL or CL mimic has a structural orfunctional similarity to a known naturally occurring CL, such as betweenNADH and AcNADH, a reactive atom of a CL can be identified by analogy tothe reactive atom of a known naturally occurring CL.

Unlike the first domain conserved among the dehydrogenases, the seconddomain can differ markedly among the individual enzymes and can bind aunique substrate from which the hydrogen is removed.

The term “specificity ligand” or “SL” herein means a molecule that canbind to a second site on the enzyme. A particularly useful SL can bindto a unique or a relatively small subset of a gene family, where thefamily shares binding properties with a single CL. Accordingly, the term“specificity ligand site” is the location where the specificity ligandcan bind to an enzyme

While specificity ligands can be naturally occurring molecules, they canalso be chemical analogs that serve as mimics to naturally occurringmolecules. These can be referred to as SL mimics, although “specificityligand” should be understood to encompass “specificity ligand mimics” aswell. Because SLs can include SL mimics that are analogs of naturallyoccurring SLs, and because the scope of the term “SL mimic” can alsoencompass the original SL itself, the scope of the terms “SL” and “SLmimic” should be considered coextensive. Specificity ligands can alsohave a reactive atom and reactive region, corresponding to the reactiveatom and reactive region defined for CLs above.

In summary, such enzymes can transfer a reactive atom between a SL boundat the SL site and a CL bound at the CL site. For example, anNAD⁺-dependent dehydrogenase can transfer a hydride ion from the SL tothe CL, which is NAD⁺.

Given the catalytic function of dehydrogenases and other enzymes, itfollows that the CL site and the SL site should be physically located inproximity in the enzyme's three-dimensional structure to facilitatetransfer of the hydrogen or other reactive atom In fact, thethree-dimensional geometric relationship between the CL site and SLsites has been shown to be conserved in evolutionarily relateddehydrogenases (Sem and Kasper, “Geometric Relationship Between theNicotinamide and Isoalloxazine Rings in NADPH-Cytochrome P450Oxidoreductase,” Biochemistry 31:3391-3398 (1992)). Thus, the CL siteand SL site are said to be “adjacent.” The domains of a protein may moverelative to each other, depending on a variety of factors, such assubstrate binding, so the protein can be described as being in an openor closed conformation. Nevertheless, in practical terms, an atom of theCL site and an atom of the SL site are at some point in time at most 3,4, 5, 6, or 7 Å apart.

The portion of the enzyme between the adjacent CL and SL sites can bedefined as the “interface region.” In FIG. 1 a, the interface region isshown schematically as 1 c Because an SL bound at the SL site can havesimilar properties as enzyme atoms of the interface region, the term“interface region” can also encompass atoms of an SL if an SL is boundto the enzyme at the SL site.

While the enzymes have been discussed in reference to dehydrogenases forpurposes of illustration, it should be understood that any other enzymewill be useful in the invention so long as (1) the enyzme can bind a CLor a CL mimic at a CL site and binds an SL at an adjacent SL site; (2)an interface region can be defined as the atoms of the enzyme betweenthe CL site and SL site, including atoms of a SL if bound to the enzyme;(3) the enzyme catalyzes a reaction mechanism involving a SL and areactive atom of a CL; and (4) a CL reactive region can be defined asthe reactive atom of the CL and CL atoms immediately adjacent to thereactive atoms or CL atoms immediately adjacent to the SL.

To prepare an enzyme for use in the method of the invention, the enzymecan be isolated or expressed by recombinant methods, harvested andpurified by any conventional method well known in the art. Aparticularly useful enzyme can be isotopically labeled with ²H, ¹³C, ¹⁵Nor any combination of these isotopes (Venters et al., “High-level²H/¹³C/¹⁵N Labeling of Proteins for NMR Studies,” J. Biomol. NMR5:339-344 (1995)). Following such labeling, deuterated amides can beexchanged with protons, depending on the particular NMR method used, asdiscussed below. A high level of amino-acid-specific protonation can bere-introduced in the protein. For example, to introduce protonation,this can be achieved by using directly protonated amino acids, oramino-acid precursors when the protein is expressed in bacteria (Rosenet al., “Selective Methyl Group Protonation of Perdeuterated Proteins,”J. Mol. Biol. 263:627-636 (1996)). The amino acids that are particularlyuseful contain methyl groups, although any amino acids can beintroduced.

Having disclosed enzymes and ligands useful in the invention, thepresent invention provides a method for identifying an atom of a commonligand mimic that is proximal to an interface region. The methodcomprises two separate stages. In the first stage, an atom of theinterface region is identified that is proximal to the reactive regionof the common ligand. Second, the atom identified in the first stage isused to identify an atom in the CL mimic that is proximal to theinterface region. Because this atom will also be proximal to the SLsite, the atom or immediately adjacent atoms can then serve as anoptimal point of variation when generating a combinatorial library ofbi-ligand compounds that can bind at both the CL and the SL sites.

The first stage is performed by binding a CL to the CL site of theenzyme. The SL may also be bound to the enzyme. Then, an atom of the CLreactive region is perturbed by any of the various methods disclosed infurther detail below. Thus, an interface atom can be identified that isperturbed by the perturbation of the CL reactive region, and hence isproximal to the CL.

In the second stage, a CL mimic is bound to the CL site. Again, the SLmay be bound to the enzyme. The interface atom identified during thefirst stage is then perturbed As in the first stage, this perturbationthen causes further perturbation in nearby atoms in the CL mimic, whichcan also be detected, thereby identifying an atom of the CL mimic thatis proximal to the interface region

As a comparison, atoms of the CL mimic that are not proximal to theinterface atom do not become perturbed during the second stage.Similarly, if a CL mimic is bound to the CL site so that its atoms arenot proximal to the interface region, the CL mimic atoms will also notbecome perturbed. Thus, only proximal atoms of the CL mimic areidentified.

In addition to the general method for identifying proximal atomsdisclosed above, several variations are also encompassed within theinvention. These variant methods also provide the identity of atoms inthe common ligand or CL mimic that are proximal to the interface regionof the enzyme, and therefore also proximal to the SL site.

Where an atom of the interface region has already been identified in theenzyme, the method can proceed directly to the second stage. Suchidentification can be by any means available, such as by homologymodeling, mutagenesis or limited assignment. Thus, the method cancomprise the steps of (1) binding a CL mimic to the CL site; (2)perturbing the identified atom of the interface region; and (3)identifying an NMR cross-peak corresponding to an atom of the CL mimicthat is perturbed by the perturbation of the interface atom, therebyidentifying an atom of the CL mimic that is proximal to the interfaceregion.

Another variation makes use of transient binding of CL and CL mimics atthe CL site of the enzyme in a transferred NOE experiment. As shown inFIG. 5 a, a CL is bound to the CL site in the presence of unbound CLmimic. An atom of the CL can be perturbed by radiofrequency irradiationin an NOE experiment so that energy is transferred from the reactiveregion CL atom to the interface region. The CL is then allowed tounbind, as shown in FIG. 5 b. When a CL mimic binds at the same CL site,as shown in FIG. 5 c, magnetization is transferred back from theinterface region to perturb an atom in the CL mimic, as shown in FIG. 5d. As a result, an NMR cross-peak can be identified corresponding to theatom of the CL mimic proximal to the interface region.

Yet another variation involves the observation of NOEs on dissociatedligands. An interface atom of the enzyme is perturbed, for example byirradiation, followed by magnetization transfer to CL mimic bound to theenzyme. Upon dissociation of the CL mimic from the enzyme, the NOE canthen be observed before magnetization decay in the nonbound CL mimic.Thus, an atom of the dissociated CL mimic can be identified that wasproximal to the interface region when bound to the CL site.

The term “perturb” herein means to affect the chemical shift, intensityor lineshape of the NMR signal for a nucleus so that the effect can bedetected in an NMR experiment. Perturbation also includes causing adetectable change in nuclear spin relaxation rates (1/T2 and 1/T1).

A particular perturbation method is to chemically alter an atom or animmediately adjacent atom. An example is the chemical substitution ofreactive region atoms, such as replacing hydrogen with deuterium.Another substitution is replacing an amide with a carboxylic acid. Thesesubstitutions alter the electronic and structural environment of nearbyatoms in the interface region, which produces changes in their NMRchemical shifts. Other chemical alterations include the introduction ofparamagnetic or quadrupolar nuclei.

For example, a reactive hydrogen in NADH or NADPH can be perturbed byreplacing the hydrogen with deuterium, resulting in NADD or NADPD (Semand Kasper, “Geometric Relationship between the Nicotinamide andIsoalloxazine Rings in NADPH-Cytochrome P-450 Oxidoreductase:Implications for the Classification of Evolutionarily and FunctionallyRelated Flavoproteins,” Biochemistry 31: 3391-3398 (1992)). In thissense, the perturbation from NADH to NADD can be considered to be eitherthe chemical alteration itself or the particular differences in the NMRspectra of an enzyme binding NADH and the NMR spectra of an enzymebinding NADD. Similarly, an atom of the enzyme can be perturbed bysite-directed mutagenesis so that the differences between the spectra ofthe original enzyme and the mutated enzyme can be detected.

Yet another method of perturbation is to irradiate an atom with radiofrequency energy (Rf irradiation). The term “radio frequency energy”herein means oscillating electrical voltages, currents orelectromagnetic fields with frequencies in the range of 10 to 1000 MHZor 10⁷ to 10⁹ sec¹. The frequency selected depends on the magnetic fieldstrength and the corresponding Larmor frequency for the nucleus ofinterest at that field strength. Thus, differences in NMR spectra can beobserved in samples with and without irradiation.

In modern multidimensional NMR NOE experiments, excitation is performedat a range of frequencies simultaneously so that frequencies are readoff axes in each dimension. The central frequency and frequency range isselected for a given nucleus type so that it will excite all of thosenuclei in the molecule. For example, at an 11.7 Tesla magnetic fieldstrength, protons are excited at 500.0 MHZ (the Larmor frequency),. witha range of at least±5000 Hz.

As a result of perturbing a particular atom, other nearby atoms can beperturbed as well. The nuclear Overhauser effect (NOE) can causedetectible changes in the NMR signal of an atom that is proximal to theperturbed atom. Here, NOE is meant to include steady state and transientNOE. The signal changes are the result of magnetization transfer to theproximal atoms. Since an NOE occurs by spatial proximity, not merelyconnection via chemical bonds, it is especially useful for determiningdistances between molecules. The term “proximal” herein means within adefined distance of one or more atoms of interest, where the defineddistance is a function of the method used to perturb. Functionally,“proximal” can be defined as being within a distance where perturbationcan be detected. When an NOE is used, the distance is usually 5ÅAngstroms, but can be 2, 3, 4 or 6, 7 or 8 Ångstroms.

Perturbation—whether by chemical alteration of an atom or as a result ofirradiation in an NOE experiment—can be detected and identified by avariety of known methods. Detectable changes in NMR signals includechanges in intensity (NOE), location (chemical shift) or width(linewidth). General NMR techniques for proteins, includingmultidimensional NMR experiments and determination of protein-ligandinteractions can be found in David G. Reid (ed.), Protein NMRTechniques, Humana Press, Totowa N.J. (1997).

In practice, the perturbed atoms in large molecules can be identifiedusing a multidimensional multinuclear NMR method to identify NMRcross-peaks corresponding to the perturbed atoms. Heteronuclear NMRexperiments are particularly useful with larger proteins as described inCavanaugh et al., Protein NMR Spectroscopy: Principles and Practice, ch.7, Academic Press, San Diego Calif. (1996). For example, two-dimensionalNMR experiments can measure the chemical shifts of two types of nuclei.A well established 2-D method is the ¹H-¹⁵N heteronuclear single quantumcoherence (HSQC) experiment. Another method is the heteronuclearmultiple quantum coherence (HMQC) experiment. Numerous other variantexperiments and modifications are known in the art including nuclearOverhauser enhancement spectroscopy experiments (NOESY), for example NOEexperiments involving a {¹H,¹H} NOESY step.

Ambiguity based on chemical shift overlap can be resolved by (a)introducing a third dimension for ¹⁵N or ¹³C chemical shift; (b) notdecoupling to a heteroatom in one of the two dimensions, thus producingdiagnostic ¹H-¹³C or ¹H-¹⁵N one bond coupling constants; or (c) using2-D ¹³C-¹H or ¹⁵N-¹H HMQC or HSQC-{¹H,¹H} NOESY variants.

Higher-dimensional NMR experiments can be used to measure the chemicalshifts of additional types of nuclei and to eliminate problems withcross peak overlap if spectra are too crowded. In particular, the NMRmethod used can correlate ¹H, ¹³C and ¹⁵N (Kay et al., J. Magn. Reson.89:496-514 (1990); Grzesiek and Bax, J. Magn. Reson. 96:432-440(1992)),for example in an HNCA experiment. Other heteronuclear NMR experimentscan be used so long as the transfer of magnetization to all CL andprotein protons is only to or from amide protons on the protein, sinceall carbon-attached protons in the protein are replaced with deuterons.Such experiments include HNCO, HN(CO)CA, HN(CA)CO and HNCACBexperiments.

Other experiments involve cross-peaks of NH protons of protein at Asn,Gln, Arg and/or His. Similarly, the cross-peaks of the methyl protons ofprotein specifically ¹³C-¹H₃ labeled at Leu, Thr, Ile, Val, Ala and/orMet can be observed in NOESY, chemical shift perturbation or otherexperiments.

Particular multidimensional techniques for identifying compounds thatcan bind to target molecules are described in U.S. Pat. No. 5,698,401 toFesik et al., and U.S. Pat. No. 5,804,390 to Fesik et al. Relatedpublications include PCT publications WO 97/18469, WO 97/18471 and WO98/48264. However, these techniques, sometimes described as “SAR byNMR,” require the complete assignments and determination of thethree-dimensional structure of the enzyme (Shuker et al., “DiscoveringHigh-Affinity Ligands for Proteins: SAR by NMR,” Science 274:1531-1534(1996); Hajduk et al., “Discovery of Potent Nonpeptide Inhibitors ofStromelysin using SAR by NMR,” J. Am. Chem. Soc. 119:5818-5827 (1997)).As a result, identification of suitable ligands using SAR by NMR can bean undertaking of more than a year. Only by determining the multiplestructures of the enzyme while complexed with different pairs of ligandscan these techniques suggest ligands to be covalently joined and testedfor binding affinity. In contrast, the method of the invention does notrequire determining the complete assignments or structure of the enzyme;instead, it rapidly provides sufficient information to generate afocused combinatorial library of bi-ligand inhibitors without providingexcess information.

Recent advances in NMR spectroscopy have used transverserelaxation-optimized spectroscopy (TROSY) to achieve narrow line widths,substantially increasing resolution and sensitivity of multidimensionalNMR experiments. As a result, NMR can be applied to larger moleculesthan previously possible, such as proteins up to 100 kD or larger(Pervushin et al., J. Am. Chem. Soc. 120:6394-6400 (1998); Salzman etal., “TROSY-type Triple-Resonance Experiments for Sequential NMRAssignments of Large Proteins, J. Am. Chem. Soc. 121:844-848 (1999)).Deuterium labeling and decoupling has also been used to achieve narrowline widths, further enabling NMR methods to be applied to largeproteins (Yamazaki et al., “a Suite of Triple Resonance NMR Experimentsfor the Backbone Assignments of ¹⁵N, ¹³C, ²H Labeled Proteins with HighSensitivity,” J Am. Chem. Soc. 116:11655-11666 (1994)).

Deuterium labeling is especially useful if all protons—except those onspecific methyls, such as threonines—are replaced with deuterons. Suchmethyl protons should be readily detectable, even on large proteins

Using the NMR methods disclosed above, atoms proximal to perturbed atomscan be identified in the first stage by comparing NMR spectra with andwithout perturbation. As exemplified in FIG. 6, for example, NMR spectrafrom a 2D-HSQC experiment with TROSY can be compared for NADH-bounddehydrogenase and NADD-bound dehydrogenase. By comparing the spectra,NMR cross peaks can be identified that correspond to atoms most affectedby the change in electronic and chemical environment resulting fromsubstituting deuterium for hydrogen As a result, the atoms in theNADH-binding site closest to the SL binding site, which are in theinterface region, can be identified.

In order to know which cross peaks in the uncomplexed dehydrogenasecorrespond to the perturbed cross peaks in the NADD-dehydrogenasecomplex, it may be necessary to titrate the uncomplexed dehydrogenasewith increasing concentrations of either NADH or NADD and monitorprogressive changes in chemical shifts. Such a titration is notnecessary if the corresponding cross peaks in the uncomplexeddehydrogenase can be identified by other means, such as the presence ofa unique pair of ¹³C chemical shifts in the HNCA experiment.

In the second stage, NMR spectra can be collected for the enzyme incomplex with a CL mimic. For example, a TROSY implementation of the 3D[¹H-¹⁵N] HSQC-NOESY is illustrated in FIG. 7. The third dimension,labeled “all proton chemical shifts,” identifies protons—especially onthe CL mimic—that receive an NOE-type perturbation from the protonsidentified in the first stage. The identity of these NOE-perturbedprotons on the CL mimic are easily established based on chemical shiftvalues, since all protons on the CL mimic can be assigned by standardmethods well known in the art (P. L. Rinalidi, Two Dimensional NMRSpectroscopy: Applications for Chemists and Biochemists, pages 841-872(Croasmun and Carlson, eds.), VCH Pubs, New York (1994)). Isotopefiltering can also be used in this third dimension to select only thoseprotons not attached to ¹⁵N. These NOE-perturbed protons on the CL mimicand other atoms in this region represent the optimal positions forvariation in constructing a bi-ligand library. Significantly, theoptimal position has been identified without having previouslydetermined the complete assignments or structure for the enzyme.

It may be necessary to identify which cross peaks in the enzyme-CL mimiccomplex correspond to the interface region protons identified in thefirst stage. This can be achieved by titrating the CL mimic onto thedehydrogenase and monitoring how the cross peak changes for thepreviously identified proton. Again, such experiments are not necessaryif the cross peaks of interest can be identified by other means.

In summary, to facilitate the catalytic mechanism of an enzyme, an atomof the reactive region of a bound common ligand will be proximal to theSL site and the intervening interface region. The reactive region canthen be used to identify proximal atoms in the interface region. Inturn, by virtue of the proximity between the interface region and the CLsite, the interface region can be used to identify proximal atoms in abound common ligand mimic. Such proximal atoms will be nearest to the SLsite and provide a basis for building bi-ligands that can bind to boththe CL site and the SL site. As a corollary, the method can identify, byelimination, those atoms in the CL mimic that are too distant from theSL site to serve as useful points of variation.

In an alternate embodiment, the first stage can be performed by bindingan SL to the SL site of the enzyme; perturbing an atom of the SLcorresponding to an SL reactive region, and identifying an NMRcross-peak corresponding to an atom that is perturbed by theperturbation of the atom of the SL reactive region, thereby identifyingan atom of the interface region. The second stage can be performed bybinding an SL mimic to the SL site, perturbing the interface atompreviously identified, and identifying an NMR cross-peak correspondingto an atom of the SL mimic that is perturbed by the perturbation of theinterface atom, thereby identifying an atom of the SL mimic that isproximal to the interface region.

Thus, the following is a generalized embodiment of the invention foridentifying an atom of a first ligand mimic that is proximal to aninterface region. A given enzyme can bind a first ligand (L1) or a firstligand mimic (L1 mimic) at a first ligand site (L1 site) and can bind asecond ligand (L2) at an adjacent second ligand site (L2 site). Theinterface region can be defined as the atoms of the enzyme between theL1 site and L2 site, but also includes atoms of L2 if bound to theenzyme. An L1 reactive region is defined as the reactive atom of L1, aswell as L1 atoms immediately adjacent to the reactive atom or L1 atomsimmediately adjacent to L2. The first stage involves identifying an atomof the interface region, by binding an L1 to the L1 site of the enzyme,perturbing an atom of the L1 reactive region; and identifying an NMRcross-peak corresponding to an atom that is perturbed by theperturbation of the atom of the L1 reactive region, thereby identifyingan atom of the interface region. The second stage involves identifyingan atom in the L1 mimic that is proximal to the interface region, bybinding an L1 mimic to the L1 site; perturbing the interface atompreviously identified in the first stage; and identifying an NMRcross-peak corresponding to an atom of the L1 mimic that is perturbed bythe perturbation of the interface atom, thereby identifying an atom ofthe L1 mimic that is proximal to the interface region.

It should be noted that CL mimics may bind to different positions withina CL site. For example, a particular CL mimic 4 may bind relativelyclose to the interface region, as shown in FIG. 3 a, while another CLmimic 5 may bind distally, as shown in FIG. 3 c. By identifying atomsproximal to the interface region, the method can therefore be used toscreen for CL mimics that can bind proximally to the interface region.CL mimics like 5 that can bind distally may not contain atomssufficiently close to the interface region to be useful for generatingbi-ligand libraries.

Because the method uses NMR methods to provide structural information toengineer a bi-ligand library, the method can be termed Nuclear MagneticResonance-Structure Oriented Library Valency Engineering orNMR-SOLVE^(SM). Without NMR-SOLVE^(SM), a combinatorial library based onthe CL mimic would involve variation at potentially every point on theCL mimic. With NMR-SOLVE^(SM), the library can be focused at the optimalpoint of variation, representing a significant savings in drug discoverytime.

Thus, the present invention also provides a method for generating afocused combinatorial library of bi-ligand compounds that cansimultaneously bind to a CL site and an SL site of an enzyme. The term“combinatorial library” herein means an intentionally created set ofdiffering molecules prepared by taking a base structure and, in parallelreactions, adding different substituent groups to points on the basestructure, resulting in the parallel synthesis of compounds that arevariations on the core structure. By taking the products as corestructures in a succeeding set of parallel reactions, further variantcompounds can be generated, resulting in a diversity of relatedcompounds. As a result of the combinatorial process, the products aregenerally prepared in essentially equimolar quantities, considering ofcourse the different efficiencies of the individual synthetic reactions.Not included within this definition are multiple isomeric and chiralproducts and undesired by-products resulting from a single reactionscheme. Also not included are intentional or accidental mixtures oforiginally pure compounds not arising out of the combinatorial syntheticprocess.

A number of formats for generating combinatorial libraries are wellknown in the art, for example soluble libraries, compounds attached toresin beads, silica chips or other solid supports. As an example, the“split resin approach” may be used, as described in U.S. Pat. No.5,010,175 to Rutter and in Gallop et al., J. Med. Chem., 37:1233-1251(1994).

The term “substituent group” herein means any chemical compound orfunctional group that can be synthetically attached to a base structure.Examples of substituent groups suitable for addition to a base structureinclude halo, hydroxy and protected hydroxyls, cyano, nitro, C₁ to C₆alkyls, C₂ to C₇ alkenyls, C₂ to C₇ alkynyls, C₁ to C₆ substitutedalkyls, C₂ to C₇ substituted alkenyls, C₂ to C₇ substituted alkynyls, C₁to C₇ alkoxys, C₁ to C₇ acyloxys, C₁ to C₇ acyls, C₃ to C₇ cycloalkyls,C₃ to C₇ substituted cycloalkyls, C₅ to C₇ cycloalkenyls, C₅ to C₇substituted cycloalkenyls, a heterocyclic ring, C₇ to C₁₂ phenylalkyls,C₇ to C₁₂ substituted phenylalkyls, phenyl and substituted phenyls,naphthyl and substituted naphthyls, cyclic C₂ to C₇ alkylenes,substituted cyclic C₂ to C₇ alkylenes, cyclic C₂ to C₇ heteroalkylenes,substituted cyclic C₂ to C₇ heteroalkylenes, carboxyl and protectedcarboxyls, hydroxymethyl and protected hydroxymethyls, amino andprotected aminos, (monosubstituted)amino and protected(monosubstituted)aminos, (disubstituted)aminos, carboxamide andprotected carboxamides, C₁ to C₄ alkylthios, C₁ to C₄ alkylsulfonyls, C₁to C₄ alkylsulfoxides, phenylthio and substituted phenylthios,phenylsulfoxide and substituted phenylsulfoxides or phenylsulfonyl andsubstituted phenylsulfonyls. As discussed below, substituent groups canalso include compounds that are ligands to enzymes such as a SL or SLmimics, as well as linkers.

Under the method of the invention, the libraries are generated by firstperforming the methods disclosed above to identify an optimal CL mimicand a CL mimic atom that is proximal to the interface region. In FIG. 4,for example, the proximal atom 4 a has been identified. Then, compoundsare synthesized by modifying the CL mimic at the proximal atom byattaching substituent groups.

For example, a focused combinatorial library 6 has been generated byusing the proximal atom 4 a as a point of variation on the CL mimic corestructure 4. The library contains several compounds 6 a-6 d, each havinga substituent group added at the proximal atom 4 a. Thus, the term“focused” herein means a combinatorial library where substituent groupsare added to preselected points on the core structure. In contrast, anunfocused combinatorial library 7 could begin with a non-optimal CLmimic 5 or begin with the same CL mimic 4 as a core structure, but theaddition of substituent groups could occur at any point on the basestructure, for example at an atom 4 b distant from the SL site, leadingto a substantially greater number of potentially ineffective bi-ligandcompounds to be screened

Because the invention is directed to combinatorial libraries ofbi-ligand compounds, a particularly useful substituent group includes achemical moiety that can bind to the SL site of the enzyme. Theselection of such a moiety depends on the enzyme of interest, of course,but the substituent group can be an SL or SL mimic of an enzyme attachedto the core structure of the CL mimic, allowing the resulting compoundto bind to both the SL and CL sites of the enzyme.

In some enzymes, the SL and CL sites can be a short distance apart, forexample 2 Å. Nevertheless, when seeking a compound having moieties thatcan bind at both the SL and CL sites, it can be useful to incorporate alinker into the substituent group to span the distance between the twosites. The term “linker” herein means any chemical group or portion of amolecule used to physically connect one moiety to another moiety. Forexample in FIG. 4 b, a linker 9 can connect an SL-site-binding moiety 8to a CL mimic core structure 4 while maintaining the two moieties at adistance, allowing the compound 6 c to bind the enzyme 1 tightly at boththe SL site 1 a and the CL site 1 b Thus, a linker can also providepositioning and orientation of the two moieties to optimize theirbinding to their respective binding sites.

Because the resulting library of compounds can bind to both sites of theenzyme, they can be described as “bi-ligands.” The term “bi-ligand”herein means any molecule having at least two moieties where eithermoiety can bind to an enzyme independently or both moieties can bind tothe same enzyme simultaneously. In such a bi-ligand, one moiety can be aCL or CL mimic. Similarly, the other moiety can be a SL or SL mimic.Thus, the invention also provides a combinatorial library of bi-ligandcompounds obtained by the method of the invention for generating focusedlibraries. Such a library can contain at least 2, 5, 10, 15, 20 or 50bi-ligand compounds. It can also contain 100, 200, 500, 1000 or even upto 10,000 or 100,000 bi-ligand compounds.

As a result of their ability to bind at multiple sites on an enzyme, thebi-ligand compounds in the libraries can have high affinities to theenzyme. Even if two individual moieties have relatively low bindingaffinities, the combination of the two ligands in a single bi-ligandcompound can have a synergistically higher binding affinity (Radzicka &Wolfenden, “Transition State and Multisubstrate Inhibitors,” Methods inEnzymology 249:284-303 (1995)). As an example, where two weakly bindingligands having binding affinities of 17 mM and 0.02 mM were linked, theresulting compound had a much higher binding afinityh of 15 nM (Hajduket al., “Discovery of Potent Nonpeptide Inhibitors of Stromelysin usingSAR by NMR,” J. Am. Chem. Soc. 119:5818-5827 (1997)). Accordingly, suchbi-ligand compounds can be screened for their affinity to the enzyme orto other enzymes in the gene family.

Another advantage of these bi-ligand libraries is that the CL mimic canprovide a certain baseline affinity for other members of the genefamily. Further addition of a specificity ligand or SL mimic can provideadditional affinity to other particular members. Thus, the library canbe a rich source of specific bi-ligand inhibitors for multiple membersof a gene family.

Thus, the present invention further provides a method for screeninglibraries of bi-ligand compounds. After generating a combinatoriallibrary of bi-ligand compounds as disclosed above, the binding of thecompounds to the enzyme is measured. Individual compounds are thenidentified having greater binding than the CL mimic. Binding assays forenzymes and ligands are well known in the art and can be selected basedon the particular enzyme and ligands being used.

Individual bi-ligand compounds identified by this screening method arealso encompassed within the invention. In particular, such compounds canbe screened that increase or decrease the activity of the enzyme.Moreover, such compounds can have extremely high binding affinities,having binding affinities of 100, 200, 1000, 5000 or even 10,000 timesgreater than the CL mimic's binding affinity. In addition to screeningthe bi-ligand compounds for affinity to the enzyme, it can be screenedas an inhibitor for other members of the gene family. Binding toparticular enzymes can also be particularly high when compared to othermembers of the gene family, so that the compound's binding affinity canbe at least 50, 100, 200, 500, or 1000 times greater to the individualenzyme than to another enzyme in the same gene family. This specificityis provided by the binding interactions with the specificity ligands orSL mimics, since the common ligand can bind with similar affinity tomultiple members of gene family.

Once high affinity bi-ligand compounds are identified, their binding tothe enzyme at both CL and SL sites may be verified by the NMR methodsdisclosed above

EXAMPLE I NMR-SOLVE^(SM) of DHPR from Mycobacterium tuberculosis

The following example illustrates the NMR-SOLVE^(SM) method foridentifying an optimal CL mimic and an atom of a CL mimic that isproximal to the interface region of an enzyme.

The enzyme dihydrodipicolinate reductase (DHPR) from Mycobacteriumtuberculosis is selected because it plays a key role in the synthesis ofthe cell wall, and is vital for the survival of Mycobacterium (Pavelkaand Jacobs, “Biosynthesis of Diaminopimelate, the Precursor of Lysineand a Component of Peptidoglycan, is an Essential Function ofMycobacterium smegmatis,” J. Bacteriol. 178:6496-6507 (1996)).

Tuberculosis is a desirable biological target for drug design, since thegenome has recently been made available, providing a rich source of newdrug targets (Cole et al., “Deciphering the Biology of Mycobacteriumtuberculosis from the Complete Genome Sequence,” Nature 393:537-544(1998)). Moreover, tuberculosis is the leading cause of death frominfectious disease in adults (Dolin et al., “Global TuberculosisIncidence and Mortality During 1990-2000,” Bull. WHO 72:213-220 (1994)).Furthermore, tuberculosis is showing a resurgence in developing nationswith increasing reports of drug resistant strains (Snider et al.,“Global Burden of Tuberculosis,” pages 3-11, in B. R. Bloom (ed.),Tuberculosis: Pathogenesis, Protection, and Control, ASM Press, Wash.D.C. (1994)).

A. Preparation of Uniformly ¹⁵N and ¹³C-labeled DHPR, with Deuterium inNon-Exchangeable Positions

Genomic DNA from Mycobacterium tuberculosis is prepared with standardmethods (Sambrook et al., Molecular Cloning: A. Laboratory Manual, ColdSpring Harbor Laboratory, Cold Spring Harbor N.Y. (2nd ed. 1989)). TheDHPR gene is cloned using oligonucleotide primers complementary to theends of the gene from the open reading frame sequence (Pavelka et al.,“Cloning of the dapB Gene, Encoding Dihydrodipicolinate Reductase, fromMycobacterium tuberculosis, ” J. Bacteriol. 179:2777-2782(1997)(Accession number U66101)). Standard PCR reactions are used withthe GENEAMP PCR kit from Perkin Elmer (Norwalk Conn.).

The resulting fragment is cloned into both the pGEX (Pharmacia:Piscataway N.J.) and pET41 (Novagen: Madison Wis.) vectors, usingmanufacturer's instructions, with appropriate restriction enzymes forthe respective vectors. The plasmid/gene constructs are then transformedinto commercially available competent E. coli BL21(DE3)pLysS strains(Invitrogen: Carlsbad Calif.), according to the manufacturer'sinstructions. The following expression is performed on a trial basiswith each vector to empirically select for optimal expression yields.

E. coli containing the expression construct is adapted to grow in 100%D₂O using standard methods and glycerol stocks are prepared (Venters etal., “High-level ²H/¹³C/¹⁵N Labeling of Proteins for NMR Studies,” J.Biomol. NMR 5:339-344 (1995)). Expression is performed in defined mediaof 3 g/L sodium [1,2-¹³C2, 99%] acetate or 2 g/L [U-¹³ C6, 99%]D-glucose as the sole carbon source and 1 g/L [¹⁵N, 99%] ammoniumchloride or [¹⁵N, 99%] ammonium sulfate as the sole nitrogen source. Allstable isotopes are from Cambridge Isotopes, Inc (Andover Mass.) andIsotec, Inc (Miamisburg Ohio). The media also contains a modified M9salt mixture: 44 mM Na₂HPO₄, 22 mM KH₂PO₄, 9 mM NaCl, 1 mM MgSO₄, 0.1 μMCaCl₂, 0.02 μM FeCl₃ and basal medium Eagle vitamin mix (Gibco-BRL),with the appropriate antibiotic for the expression vector, such as 50μg/mL carbenecillin) All reagents are prepared in D₂O.

This media is inoculated at 37° C. from either a glycerol stock or froma freshly plated colony. When the absorbance at 600 nm reaches 0.4-0.8,DHPR production is induced by adding isopropyl-β-D-thiogalactopyranosideto a final concentration of 500 μM and incubated for 12 to 18 hours.Cells are harvested by centrifugation at 5000 rpm for 20 min at 5° C.,then lysed with sonication.

The protein is purified on a glutathione affinity column using themanufacturer's instructions, which includes removal of theglutathione-S-transferase enzyme with thrombin cleavage. The protein isalso purified with FPLC anion- or cation-exchange chromatography usingstandard procedures (Pharmacia: Piscataway N.J.). To perform experimentsrelying on ¹H-¹⁵N correlations, the solvent-exposed deuterated amidepositions are exchanged with protons by incubating the protein at pH 7.5at room temperature for 2 to 24 hours, then exchanging into a lower pHbuffer (such as 20 mM phosphate buffer at pH 6.0) at 5° C. using a PD10gel filtration column (Pharmacia) or CENTRICON 10 filter (Millipore:Bedford Mass.). Although not all amides are exchanged, thesolvent-exposed amides do exchange, and the unfilled active sites aresufficiently exposed to allow exchange. Avoiding complete exchange hasthe advantage of simplifying the 3D NMR spectra. Protein for NMRexperiments is present at 0.5-5 mM, although lower concentrations can beused with a cryoprobe (Bruker: Billerica Mass.).

B. Identification of CL Mimics

The common ligand of DHPR is NADH or NAD⁺. CL mimics are identified bydisplacement experiments. Such displacement is measured using standardsteady-state kinetic analysis where the concentration of NADH is variednear its K_(m) concentration in the presence of a single, fixedconcentration of the other substrate, dihydrodipicolinate (Reddy et al.,“Expression, Purification, and Characterization of Eschericia coliDihydrodipicolinate Reductase,” Biochemistry 34:3492-3501 (1995); Reddyet al., “Interaction of Pyridine Nucleotide Substrates with Eschericiacoli Dihydrodipicolinate Reductase: Thermodynamic and StructuralAnalysis of Binary Complexes,” Biochemistry 35:13294-13302 (1996)). Thisis repeated in the presence of several concentrations of a potential CLmimic. If Lineweaver-Burk plots (1/velocity versus 1/[NADH]) areprepared at the different concentrations of CL mimic inhibitor,according to the equation for a competitive inhibitor, an intersectingpattern will be obtained if the CL mimic binds in the NADH site(Cleland, W. W., Methods Enzymol. 63:103-138 (1979)).

It is also possible to identify CL mimics in a displacement assay thatis generally useful for multiple members of a gene family. Afluorescently labeled CL mimic is displaced by a candidate CL mimic andthe displacement is detected with fluorescence polarization (Burke etal., Phage Display of Peptides and Proteins, Academic Press, New YorkN.Y. (1996)).

The above methods disclose how CL mimic candidates are experimentallyvalidated as binding at the CL site. Molecules to be screened in such anassay can be synthesized or purchased from chemical supply houses.Commercially available molecules are preferably chosen according to somepre-selection criteria, such as by identifying those molecules presentin a database of commercially available molecules (Asinex: Moscow,Russia) that have similar shape and electronic properties to a targetstructure such as the known common ligand (NADH) or a structurallycharacterized CL mimic (such as cibacron blue).

THREEDOM software was used to search for matches against a targetstructure. THREEDOM employs a gnomonic projection algorithm forshape-matching a target structure in an INTERCHEM format 3D structurecoordinate file against a database of multiple structure/coordinates(Doucet and Weber, Computer-Aided Molecular Design: Theory andApplications, Academic Press, San Diego Calif. (1996)). The target usedto search the ASINEX database was cibacron blue. Coordinates wereobtained from the published 3D structure (Li et al., “TheThree-dimensional Structure of NAD(P)H:quinone Reductase, a FlavoproteinInvolved in Cancer Chemoprotection and Chemotherapy: Mechanism of theTwo-electron Reduction,” Proc. Natl. Acad. Sci. USA 92:8846-8850(1995)). The database was created by converting an SD format file ofstructures from ASINEX to INTERCHEM format coordinates using the batch 2to 3 program. The target is compared against each structure in thedatabase in multiple orientations to generate a matching score. Out of37,926 structures searched, the 750 best matching scores were selected.From these 750 structures, 250 are selected and purchased based onobjective criteria such as likely favorable binding interactions,pharmacophore properties, synthetic accessibility and likelypharmacokinetic, toxicological, adsorption and metabolic properties.

C. NMR-based Identification of Protein Interface Atoms

NMR experiments are performed on a Bruker 700 MHZ NMR spectrometerequipped with a ¹H/¹³C/¹⁵N triple resonance probe able to simultaneouslyperform broadband ²H decoupling and ²H locking. Triple resonanceexperiments are performed, and data are processed with standardmethodology (Cavanagh et al., Protein NMR Spectroscopy: Principles andPractice, Academic Press, New York (1996)).

A 1 mM solution of labeled (²H, ¹³C and ¹⁵N) DHPR is prepared in 95%H₂O/5% D₂O, pH 6.0 and kept at 5° C. All of the NMR experiments areperformed in the presence of a stoichiometric excess of2,6-pyridinedicarboxylate. The compound 2,6-pyridinedicarboxylate is ananalog of dihydrodipicolinate, the other DHPR substrate. The compound ispresent in excess to produce a dead-end complex that forces the enzymeinto a closed conformation so that SL-binding and CL-binding domains areproximal (Scapin et al., “Three-Dimensional Structure of Eschericia coliDihydrodipicolinate Reductase in Complex with NADH and the Inhibitor2,6-Pyridinedicarboxylate,” Biochemistry 36:15081-15088 (1997); Wang etal., “Hydrogen/Electrospray Ionization Mass Spectrometry Studies ofSubstrate and Inhibitor Binding and Conformation Changes of Escherichiacoli Dihydrodipicolinate Reductase, Biochemistry 36:3755-3759 (1997)).

3D HNCO and 3D HNCA data are collected for the binary complexes ofenzyme bound with 2,6-pyridinedicarboxylate, and for ternary complexesfurther binding NADH or NADD. In addition, 3D HNCA spectra are collectedat multiple concentrations of NADH to identify those cross peaks in thebinary complex corresponding to those in the ternary complex that aremost affected by the H to D substitution between NADH and NADD. NADD [4Rposition labeled] is prepared enzymatically from NAD⁺ and perdeuteroethanol using alcohol dehydrogenase (Sem and Kasper, “GeometricRelationship between the Nicotinamide and Isoalloxazine Rings inNADPH-Cytochrome P-450 Oxidoreductase: Implications for theClassification of Evolutionarily and Functionally RelatedFlavoproteins,” Biochemistry 31: 3391-3398 (1992)).

The experiments performed with NADD are repeated with the other NADHanalog, nicotinic acid adenine dinucleotide (reduced), which has thecarboxamide group replaced with a carboxylic acid. The reduced form isprepared enzymatically from the oxidized form of nicotinic acid adeninedinucleotide using alcohol dehydrogenase and unlabeled ethanol, asdisclosed above. Although multiple NAD(P)(H) analogs are available forthese perturbation studies, those chosen provide adequate chemical shiftperturbations for this study (Everse et al. The Pyridine NucleotideCoenzymes, Academic Press, New York N.Y. (1982)). Because the changesare made to the portion of the NADH molecule known to be closest to theSL site, the cross peaks that shift as a result of the chemical changesto NADH are therefore determined to be at the interface region betweenthe two binding sites.

HNCO and HNCA experiments (Kay et al., J. Magn. Reson. 89:496-514(1990); Grzesiek and Bax, J. Magn. Reson. 96:432-440 (1992)) wereperformed as the TROSY implementation to produce narrower line-widthsfor the ¹⁵N-¹H correlations (Salzmann et al., “TROSY in Triple ResonanceExperiments: New Perspectives for Sequential NMR Assignment of LargeProteins,” Proc. Natl. Acad. Sci. USA 95:13585-13590 (1998); Salzman etal., “TROSY-type Triple-Resonance Experiments for Sequential NMRAssignments of Large Proteins, J. Am. Chem. Soc. 121:844-848 (1999)).Deuterium labeling and decoupling is also included to produce narrowerline widths, particularly for ¹³C resonances (Yamazaki et al., “A Suiteof Triple Resonance NMR Experiments for the Backbone Assignments of ¹⁵N,¹³C, ²H Labeled Proteins with High Sensitivity,” J. Am. Chem. Soc.116:11655-11666 (1994)). Spectra are processed with both Felix (MSI: SanDiego Calif.) and NMRPipe software (NIH: Bethesda, Md.) (Delaglio etal., “NMRPipe: a Multidimensional Spectral Processing System Based onUNIX Pipes” J. Biomol. NMR 6:277-293 (1995)).

D. NMR-Based Identification of Proximal CL Mimics and Proximal Atoms onCL Mimics

NMR experiments are performed as in the first paragraph of section C. 3DHNCA data are collected at multiple concentrations of each CL mimicidentified in section B as a competitive inhibitor against NADH. At thehighest concentration of the CL mimic, two types of NOESY experimentsare performed. The first is a TROSY implementation of the 3D [¹H-¹⁵N]HSQC-NOESY. Since there is significant cross-peak overlap in the 3Dexperiment, 4D versions of the HNCA and HNCO experiments are alsoperformed (Kay et al., “Four-Dimensional Heteronuclear Triple-ResonanceNMR Spectroscopy of Interleukin-1b/in Solution,” Science 249: 411-414(1990)). The 4th dimension is for NOEs from the ¹⁵N-attached protons toany other proton. The NOEs of interest are those from the perturbedcross-peaks identified in section C to any protons on the CL mimic beingstudied. These protons therefore represent optimal positions on the CLmimic for library expansion by attaching linkers.

E. Linker Attachment and Validation

Once a linker is synthetically attached to the CL mimic according toatoms of interest identified in section D, NMR experiments are performedon the DHPR ternary complex with 2,6-pyridinedicarboxylate and themodified CL mimic. NMR experiments are performed as in the firstparagraph of section C. 3D HNCA data are collected at multipleconcentrations of the modified CL mimic (with linker attached), asdisclosed in section D. These cross-peak perturbations are compared withthose observed in previous (section D) experiments with the originalunmodified CL mimic. From these data it is established that the modifiedCL mimic contacts the same binding site atoms in both complexes.Additional cross-peak perturbations due to attachment of a linker shouldalso correspond to some of the interface atoms identified in section C.

In addition to NMR experiments, steady-state inhibition experiments areperformed as disclosed in section B to establish that the modified CLmimic is still a competitive inhibitor against NADH, and to determinethe dissociation constant with DHPR to establish that adding the linkerdoes not significantly disrupt the strength of the binding interactionswith DHPR.

EXAMPLE II NMR-SOLVE^(SM) of DHPR from Escherichia coli

Given the similarity of DHPR protein sequences in Mycobacteriumtuberculosis and Escherichia coli, and the higher levels of expressionin E. coli, DHPR from E. coli was used in the following example.

The common ligand for DHPR was NADH (FIG. 9 b) and the specificityligand was dihydrodipicolinate. An analog of NADH, AcNADH (FIG. 9 c) wasused for chemical perturbation experiments. Similarly, an analog ofspecificity ligand dihydrodipicolinate was used: SL analog2,6-pyridinedicarboxylate (2,6-PDC) (FIG. 9 a).

A. Preparation of Uniformly ¹⁵N-labeled DHPR, with Deuterium inNon-Exchangeable Positions, Except Threonines, which were ¹³CH₃-Labeled

1. Expression and Isotopic Enrichment of DHPR

DHPR was prepared that was uniformly enriched in ²H and ¹⁵N andcontaining ¹H/¹⁵N/¹³C-labeled threonine residues. 2 mL LB media with 100mg/mL carbenicillin was inoculated aseptically with 20 mL of a glycerolstock of E. coli containing the pET11a+/DHPR expression construct (Reddyet al., supra). This culture was grown to OD₆₀₀ 0.4-0.5 at 37° C. Cellswere then conditioned to grow on deuterated media The first step was a50-fold dilution of the LB culture into 2 mL of 90% D₂O from CambridgeIsotope Laboratories or Isotec, Inc. in minimal media containing 5 g/LD-glucose, 2 g/L NH₄Cl, 10.725 g/L Na₂.HPO₄.H₂O, 4.5 g/L KH₂PO₄, 0.75g/L NaCl, 2 mM MgSO₄ and 2 mL (1×) of the following trace metal andnutrient solution: 2 mg/mL CaCl₂, 2 mg/mL ZnSO₄.7H₂O, 15 mg/mL thiamine,10 mg/mL niacinamide, 1 mg/mL biotin, 1 mg/mL choline chloride, 1 mg/mLpantotenic acid, 1 mg/mL pyridoxine, 1 mg/mL folic acid, 10.8 mg/mLFeCl₃.6H₂O, 0.7 mg/mL Na₂MoO₄.2H₂O, 0.8 mg/mL CuSO₄.5H₂O and 0.2 mg/mLH₃BO₃.

This culture was grown to OD₆₀₀ 0.3-0.4 at 37° C. and then diluted40-fold into 5 mL of 100% D₂O M9 minimal media, which was identical tothe media above except the D-glucose was uniformly ²H-enriched (MartekBiosciences Corp.: Columbia Md.) and the ammonium chloride was uniformly¹⁵N-enriched (Martek). This 5 mL culture was grown overnight and thenused to inoculate 100 mL of the same media. The 100 mL culture was grownat 37° C. in a 1L baffled shaker flask for 16 hours to a final OD₆₀₀ of4.5-5.0.

Protein expression was then carried out on a 1L scale in a BIOFLOW 3000fermentor (New England Biolabs: Beverly Mass.). The pH of the culturewas monitored via a gel-filled pH probe and maintained at pH 7.0 by theautomated feeding of 0.1N NaOD. The culture was aerated by continuoussparging of dried air at a flow rate of 5 L/minute. The temperature wasmaintained at 37° C. via a recirculating chiller, and the dissolvedoxygen level was monitored via a D.O. probe.

The 100 mL shaker flask culture was used to inoculate 1L basalfermentation media containing 2 gm/L ²H-D-glucose, 0.8 g/L ⁵NH₄Cl and0.5× of the trace metal and vitamin mix. The culture was grown until thepH feed was inactive and the dissolved oxygen level began to rise, atwhich time a batch-feed solution was added, consisting of 3 gm/L²H-D-glucose, 1.2gm/L ¹⁵NH₄Cl, 0.5× of the trace metal and vitamin mixand 100 mg U-²H/¹⁵N/¹³C-labeled threonine (Cambridge). After are-equilibration period of 10 to 15 minutes, protein expression wasinduced by adding 2 mM IPTG. The induction phase was carried out untilthe pH feed was inactive and the pH value began to rise with final celldensities ranging from OD₆₀₀ 4-5. The cells were then pelleted at5000×g, 4° C. for 10 minutes in four 250 mL fractions and frozen at −80°C.

2. Purification

The cell pellet from one of the fractions was resuspended in 250 mLice-cold lysis buffer consisting of 50 mM Tris pH 7.5, 100 mM NaCl, 1 mMEDTA, and 1 mL protease inhibitor cocktail. The resuspended cell pelletwas homogenized for 3 minutes. The homogenized, resuspended cells werethen lysed by three passes at 18,000 PSI through a microfluidizer. Thesoluble fraction was separated from the insoluble cellular debris bycentrifugation at 20,000×g, 4° C. for 45 minutes. The supernatant wasthen dialyzed against 2L of 50 mM Tris pH 7.8, 1 mM EDTA for 4 hours andsubsequently cleared by centrifugation at 20,000×g, 4° C. for 45minutes.

The cleared, dialyzed soluble cellular fraction was then loaded on a 100mL EAST FLOW Q-SEPHAROSE quaternary ammonium ion exchange column(Pharmacia), that had been equilibrated in 25 mM Tris pH 7.8, 1 mM EDTA.The column was washed extensively with equilibration buffer, and theprotein eluted in 5 mL fractions with a 1L 0-1 M NaCl gradient at a flowrate of 1 mL/minute. Eluted fractions were analyzed by SDS-PAGE.Fractions containing significant levels of DHPR were pooled and loadedin two fractions onto 50 mL FAST FLOW BLUE SEPHAROSE 6 dye-affinitycolumn (Pharmacia), which had been equilibrated in 20 mM Tris pH 7.8, 1mM EDTA. The column was washed with 2 column volumes of equilibrationbuffer and the protein was eluted with equilibration buffer containing2M NaCl. Approximately 200 mg/L of >99%, pure DHPR was obtained,representing a yield of about 150 mg/L.

The protein was ¹³CH₃-labeled at threonine positions so thatNMR-observable atoms were present on the protein in addition to amides.Thus, NMR-SOLVE experiments could be performed that involved eitherbackbone amides in ¹H-¹⁵N correlation spectra or at methyl groups ofthreonines in ¹H-³C correlation spectra. Narrow line widths wereobtained in ¹H-¹⁵N correlation spectra by using the TROSY pulse sequence(Salzman et al. (1998) supra; Salzman et al. (1999) supra; Wider andWuethrich, “NMR spectroscopy of large molecules and multimolecularassemblies in solution” Current Opinion in Structural Biology 9:594-601(1999)). In ¹H-¹³C correlation spectra, narrow line widths were obtainedbecause of the fast rotation of methyl protons. Methyl protons have theadded advantage of increased sensitivity because of the presence ofthree equivalent protons. Specific labeling of residues, such asthreonines, has the advantage of simplifying 2D-NMR spectra.

B. Identification of CL Mimics

CL mimics for DHPR include NADH, NAD, NADPH or NADP. Mimics of NADH orNAD were obtained by screening for displacement of the natural commonligand with the enzyme lactate dehydrogenase (LDH). Such displacementwas measured using standard steady-state kinetic analysis, where NADHwas varied around its K_(m) in the presence of a single fixedconcentration of the other substrate, pyruvate (Zewe and Fromm,Biochemistry 4:782-792 (1965)). This was repeated in the presence ofseveral concentrations of a potential CL mimic.

When Lineweaver-Burk plots (1/rate versus 1/[NADH]) were drawn at thedifferent concentrations of CL mimic inhibitor, an intersecting patternwould be obtained if the CL mimic was binding in the NADH site,according to the equation for a competitive inhibitor (Cleland, supra)It was also possible to identify CL mimics in a generally useful (acrossa gene family) displacement assay: a fluorescently labeled CL mimic wasdisplaced by a candidate CL mimic. The displacement was detected withfluorescence polarization. This can be performed in the same manner aswith peptides (Burke et al., supra), but with CL mimics

The method above describes how CL mimic candidates were experimentallyvalidated for binding in the CL site. Molecules to be screened in suchassays were synthesized or purchased from chemical supply houses. Thecandidates were pre-selected by computationally identifying moleculespresent in a database of commercially available molecules (ASINEX:Moscow, Russia) that had similar shape and electronic properties toeither the known common ligand, NADH, or a structurally characterized CLmimic, such as cibacron blue.

THREEDOM software (Interprobe Chemical Services: Glasgow, Scotland) wasused to perform this search for matches against a target structure.THREEDOM employed a gnomonic projection algorithm (Doucet and Webersupra) for shape-matching a target structure in an Interchem-format3D-structure coordinate file (Interprobe Chemical Services: Glasgow,Scotland) against a database of multiple structures/coordinates Thetarget used to search the ASINEX database was cibacron blue. Coordinateswere obtained from the published 3D structure (Li et al. supra) Thedatabase was created by converting an SD format file of structures fromASINEX to Interchem format coordinates using the batch 2 to 3 program(Interprobe Chemical Services).

The target was compared against each structure in the database inmultiple orientations, and a matching score was generated for theoptimal orientation and overlay Out of 74,500 structures searched, the1244 with best matching scores were selected and purchased. Thesecompounds were screened in the above-mentioned steady-state inhibitionassay with LDH. One of the inhibitors identified, designated asTTE0001.002.D2, is shown in FIG. 8 a.

The inhibition profile for that compound is shown in FIG. 8 b. TheLineweaver-Burk plot for the compound with lactate dehydrogenase wasplotted showing 1/[NADH] (μM)⁻¹ on the horizontal axis versus 1/rate(min/Abs) on the vertical axis. Reactions were carried out in 0.1M HEPESbuffer pH 7.4, 2.5 mM pyruvate and 5 μg/μL LDH, with DMSO kept fixed at3%. NADH was varied at 5.4, 7.0, 10.1, and 20.1 μM, and the compound waspresent at 0 (solid circles), 6.9 (open circles), 13.7 (closedtriangles) and 20.6 μM (open triangles). Initial rates were measured bymonitoring absorbance changes at 340 nm. The competitive inhibitionpattern indicated that it bound in the NADH (common ligand) site with adissociation constant of 2.1±0.4 μM.

C. NMR-Based Identification of Protein Interface Atoms

NMR experiments were performed on a 700 MHZ NMR spectrometer (BrukerNMR: Fremont Calif.) equipped with a ¹H/¹³C/¹⁵N triple resonance probeable to simultaneously perform broadband ²H decoupling and ²H locking.Multiple resonance experiments were performed. Data were processed withstandard methodology (Cavanagh et al. supra). Most experiments wereperformed with about 1 mM DHPR samples at about pH 7.5, 25 mM Tris-d₁₁buffer in 99% D₂O or in 95% H₂O/5% D₂O, with sample at 30° C. ¹³C-¹Hcorrelation experiments were obtained via HMQC magnetization transferbecause it was more sensitive than HSQC for the particular samples.Adiabatic WURST ¹³C^(β) decoupling was applied during the ¹³C t1evolution time. A 5 ms WURST-10 adiabatic pulse shifted at 70 ppm wasapplied to decouple ¹³C^(γ) from ¹³Cβ. Typically, 100*2048 complexpoints were acquired with 16 to 32 scans per increment, with a totaltime between about 1 to 2 h per HMQC experiment. Typical 2D [¹H,¹H]NOESY were acquired with 256*2048 complex points and with mixing timesbetween 100 ms and 500 ms. ¹³C^(γ) decoupling during t1 evolution wasachieved with a ¹³C 180 degree refocusing pulse. ¹³C decoupling duringthe acquisition was achieved with a GARP composite decoupling sequence.The measuring time for a 2D [¹H,¹H] NOESY varied from about 12 to 48 h.

Ligand characterization and structure elucidation was accomplished withstandard 1D ¹H and 1D ¹³C NMR, as well as 2D [¹H,¹H] COSY and, in somecases, 2D [¹H,¹H] ROESY. Frequently, NMR experiments were performed inthe presence of 3 mM 2,6-pyridinedicarboxylate (2,6-PDC), to produce adead-end complex that would force the enzyme into a closed conformation(Scapin et al. supra; Wang et al. supra). 2,6-pyridinedicarboxylate(FIG. 9 a) was an analog of the other substrate, dihydrodipicolinate.Substrate and cofactor domains of dehydrogenases most frequently adopt aclosed conformation where both domains are proximal and when bothligands are bound.

2D ¹H-¹³C HSQC data were collected for the enzyme without ligand bound(FIG. 10 a), and for the binary complex with NADH (FIGS. 9 b and 10 b)or the binary complex with 3-acetylpyridine adenine dinucleotide(AcNADH) (FIGS. 9 c and 10 c). In addition, spectra were collected atmultiple concentrations of NADH or AcNADH to identify cross peaks in theapo enzyme corresponding to the binary complex that were most affectedby the amine-to-methyl substitution in going from NADH (FIGS. 9 b and 10b) to AcNADH (FIGS. 9 c and 10 c).

Although multiple NAD(P)(H) analogs are available for these perturbationstudies (Everse et al. supra), AcNADH provided adequate chemical shiftperturbations for this study. The protein cross peaks that shifted as aresult of the chemical changes to the NADH molecule were at theinterface of the two binding sites, since the changes were made to apart of the NADH molecule known to be proximal to the specific bindingsite. Two protein cross-peaks were perturbed by the amine (FIG. 9 b) tomethyl (FIG. 9 c) substitution on NADH, shown by comparing FIGS. 10 band 10 c. Those effects were quantified in FIG. 11.

In addition to chemically perturbing the common ligand NADH and lookingfor an effect on protein, protons on AcNADH were also perturbed byirradiation, as in a standard 2D NOESY experiment (FIG. 12), and lookingfor effects on the protein in the form of an NOE, as indicated by across-peak between the AcNADH protons and protons on the proteincorresponding to cross-peak #2 in FIGS. 9 c and 10 c.

In this case, because of the specific labeling of the protein, theprotons on the protein were the methyl protons of threonines. Thecombination of these two experiments unambiguously identified cross-peak#2 as corresponding to atoms at the interface of the CL (NADH) site andSL site. Furthermore, perturbation by irradiation of the interface atomson the other ligand, 2,6-PDC, also produced NOEs to cross-peak #2 in theternary complex, further confirming its assignment as corresponding toan interface atom. It should be noted that the additional NOEs in FIG.11 from the H8A and H1′A protons of AcNADH were to another threoninemethyl that was in a part of the CL site, which was more remote from theinterface region.

D. NMR-Based Identification of Proximal CL Mimics and Proximal Atoms onCL Mimics

CL mimic protons were first assigned based on 2D-COSY data beforebinding the CL mimic to the DHPR protein, and also in the presence ofprotein. NMR experiments were performed as in the first paragraph ofsection C. 2D ¹H-¹³C HMQC data were collected at multiple concentrationsof the CL mimic identified in section B. At the highest concentration ofthe CL mimic, a 2D-NOESY experiment was carried out with a mixing timeof 200 msec (FIG. 13). The NOEs of interest were from the perturbedinterface cross-peak identified in section C to any protons on the CLmimic being studied. NOEs from the interface atom identified ascross-peak #2 matched only the H1 proton of the CL mimic TTE0001.002.D2.This confirmed the assignment of the H1 proton as an atom proximal tothe interface region. As shown, NOEs are also observed from theinterface atom identified as cross-peak #2 to bound SL analog 2,6-PDC.Also, perturbation of the interface atoms on the 2,6-PDC produced an NOEto the H1 proton of the CL mimic.

Thus, proton H1 represents the optimal region of the CL mimicTTE0001.002.D2 to attach a linker for bi-ligand library expansion, sothat diversity elements can be geometrically directed into the SL site.

Each of the references and U.S. Patents cited above is herebyincorporated herein by reference.

Although the present invention has been exemplified by the disclosedembodiments, those skilled in the art will readily appreciate that thespecific examples are provided to illustrate, not to limit, theinvention. Thus, while bacterial enzymes have been presented forpurposes of illustration, the methods of the invention may be readilyapplied to identifying drug candidates effective against enzymesinvolved in other diseases where inhibition of bi-ligand enzymes wouldbe advantageous, for example cancer, cardiovascular disease and othermicrobial and viral infections such as HIV. It should therefore beunderstood that various modifications can be made without departing fromthe spirit of the invention. Accordingly, the invention is limited onlyby the following claims.

1. A method for identifying an atom of a common ligand mimic that isproximal to an interface region; wherein the enzyme can bind a commonligand (CL) or a common ligand mimic (CL mimic) at a common ligand site(CL site) and can bind a specificity ligand (SL) at an adjacentspecificity ligand site (SL site); wherein an interface region isdefined as the atoms of the enzyme between the CL site and SL site, andatoms of an SL if bound to the enzyme; wherein the enzyme can catalyze areaction mechanism involving the SL and a reactive atom of the CL; andwherein a CL reactive region is defined as the reactive atom of the CLand CL atoms immediately adjacent to the reactive atom or CL atomsimmediately adjacent to the SL; comprising the steps of (a) identifyingan atom of the interface region, comprising the steps of (1) binding aCL to the CL site of the enzyme; (2) perturbing an atom of the CLreactive region; and (3) identifying an NMR cross-peak corresponding toan atom that is perturbed by the perturbation of the atom of the CLreactive region, thereby identifying an atom of the interface region;then (b) identifying an atom in the CL mimic that is proximal to theinterface region, comprising the steps of (1) binding a CL mimic to theCL site; (2) perturbing the interface atom identified in step (a); and(3) identifying an NMR cross-peak corresponding to an atom of the CLmimic that is perturbed by the perturbation of the interface atom,thereby identifying an atom of the CL mimic that is proximal to theinterface region.
 2. The method of claim 1, wherein the enzyme has amonomer molecular weight greater than 20 kD.
 3. The method of claim 2,wherein the enzyme has a monomer molecular weight greater than 35 kD. 4.The method of claim 1, wherein the enzyme has a complete molecularweight greater than 50 kD.
 5. The method of claim 4, wherein the enzymehas a complete molecular weight greater than 100 kD.
 6. The method ofclaim 1, wherein the enzyme is from a human pathogen.
 7. The method ofclaim 1, wherein the enzyme is from bacteria.
 8. The method of claim 1,wherein the enzyme is a dehydrogenase.
 9. The method of claim 1, whereinthe enzyme is a kinase.
 10. The method of claim 1, wherein the atom ofthe interface region in step (b)(2) is an atom of the enzyme.
 11. Themethod of claim 1, wherein the atom of the interface region in step(b)(2) is an atom of an SL bound to the enzyme.
 12. The method of claim1, wherein the CL is a cofactor.
 13. The method of claim 12, wherein theCL is SAM (S-adenosyl methionine).
 14. The method of claim 12, whereinthe cofactor contains a nucleotide.
 15. The method of claim 14, whereinthe CL is selected from the group consisting of NAD.sup.+, NADH,NADP.sup.+, NADPH, ATP and ADP.
 16. The method of claim 12, wherein theCL is selected from the group consisting of farnesyl, geranyl,geranyl-geranyl and ubiquitin.
 17. The method of claim 1, wherein theatom of the CL reactive region in step (a)(2) is the reactive atom ofthe CL.
 18. The method of claim 1, wherein the atom of the reactiveregion in step (a)(2) is a CL atom immediately adjacent to the reactiveatom.
 19. The method of claim 1, wherein the atom of the reactive regionin step (a)(2) is a CL atom immediately adjacent to the SL.
 20. Themethod of claim 1, wherein a perturbing step is achieved by chemicallyaltering an atom. 21-58. (canceled)